Published in J Am Chem Soc on February 03, 2010
SHIFTX2: significantly improved protein chemical shift prediction. J Biomol NMR (2011) 2.47
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
Accessing a hidden conformation of the maltose binding protein using accelerated molecular dynamics. PLoS Comput Biol (2011) 1.16
Interpreting protein structural dynamics from NMR chemical shifts. J Am Chem Soc (2012) 1.08
Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. J Phys Chem Lett (2011) 1.07
Dynamics and calcium association to the N-terminal regulatory domain of human cardiac troponin C: a multiscale computational study. J Phys Chem B (2012) 1.06
Biomolecularmodeling and simulation: a field coming of age. Q Rev Biophys (2011) 1.06
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. J Chem Theory Comput (2011) 1.05
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. J Chem Theory Comput (2010) 1.02
Describing sequence-ensemble relationships for intrinsically disordered proteins. Biochem J (2013) 1.00
Resolving the complex role of enzyme conformational dynamics in catalytic function. Proc Natl Acad Sci U S A (2012) 0.99
Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. J Chem Theory Comput (2011) 0.97
Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design. Chem Biol Drug Des (2013) 0.97
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J Biomol NMR (2012) 0.94
Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism. Proc Natl Acad Sci U S A (2014) 0.92
On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations. J Chem Theory Comput (2011) 0.88
Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. J Chem Phys (2011) 0.86
PPM_One: a static protein structure based chemical shift predictor. J Biomol NMR (2015) 0.83
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction. J Biomol NMR (2012) 0.83
Improved chemical shift prediction by Rosetta conformational sampling. J Biomol NMR (2012) 0.82
Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods. J Biomol NMR (2013) 0.79
Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4. J Chem Theory Comput (2013) 0.77
P.Arg82Leu von Hippel-Lindau (VHL) gene mutation among three members of a family with familial bilateral pheochromocytoma in India: molecular analysis and in silico characterization. PLoS One (2013) 0.76
Molecular-level simulation of pandemic influenza glycoproteins. Methods Mol Biol (2012) 0.75
Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. J Biomol NMR (2014) 0.75
Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD. J Chem Theory Comput (2016) 0.75
I kappa B: a specific inhibitor of the NF-kappa B transcription factor. Science (1988) 16.40
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR (2009) 16.09
Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science (1997) 9.39
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution. Science (2008) 8.04
Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci U S A (2008) 6.76
Structure of an IkappaBalpha/NF-kappaB complex. Cell (1998) 5.67
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts. J Biomol NMR (2003) 4.39
Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci U S A (2007) 3.96
Automated prediction of 15N, 13Calpha, 13Cbeta and 13C' chemical shifts in proteins using a density functional database. J Biomol NMR (2001) 3.26
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR (2007) 3.20
A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc (2005) 3.15
Use of chemical shifts in macromolecular structure determination. Methods Enzymol (2001) 2.91
NMR structures of biomolecules using field oriented media and residual dipolar couplings. Q Rev Biophys (2000) 2.90
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. Proc Natl Acad Sci U S A (2005) 2.35
Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J Am Chem Soc (2001) 2.05
Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J Am Chem Soc (2007) 2.04
A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J Am Chem Soc (2002) 1.70
Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry (2004) 1.59
Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55
Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints. J Mol Biol (1994) 1.29
Fast peptidyl cis-trans isomerization within the flexible Gly-rich flaps of HIV-1 protease. J Am Chem Soc (2005) 1.23
Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings. J Am Chem Soc (2006) 1.22
Functional dynamics of the folded ankyrin repeats of I kappa B alpha revealed by nuclear magnetic resonance. Biochemistry (2009) 1.14
The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol (1998) 1.10
Interpretation of chemical shifts and coupling constants in macromolecules. Curr Opin Struct Biol (2000) 1.01
Structural dynamics of protein backbone phi angles: extended molecular dynamics simulations versus experimental (3) J scalar couplings. J Biomol NMR (2009) 0.98
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res (2004) 11.53
Molecular dynamics simulations of biomolecules. Nat Struct Biol (2002) 7.68
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations. Biophys J (2004) 6.67
Structural characterization of flexible proteins using small-angle X-ray scattering. J Am Chem Soc (2007) 6.53
Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. J Chem Phys (2004) 5.00
Bio3d: an R package for the comparative analysis of protein structures. Bioinformatics (2006) 4.44
Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev (2006) 3.18
Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J (2004) 2.69
Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J Am Chem Soc (2002) 2.58
Constant pH molecular dynamics in generalized Born implicit solvent. J Comput Chem (2004) 2.43
Identification of slow correlated motions in proteins using residual dipolar and hydrogen-bond scalar couplings. Proc Natl Acad Sci U S A (2005) 2.35
HIV-1 protease molecular dynamics of a wild-type and of the V82F/I84V mutant: possible contributions to drug resistance and a potential new target site for drugs. Protein Sci (2004) 2.34
Localizing frustration in native proteins and protein assemblies. Proc Natl Acad Sci U S A (2007) 2.33
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering. Proc Natl Acad Sci U S A (2005) 2.28
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des (2008) 2.16
Order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc Natl Acad Sci U S A (2006) 2.15
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Structure of tumor suppressor p53 and its intrinsically disordered N-terminal transactivation domain. Proc Natl Acad Sci U S A (2008) 2.14
Generalized Born model with a simple, robust molecular volume correction. J Chem Theory Comput (2007) 2.10
Discovery of a novel binding trench in HIV integrase. J Med Chem (2004) 2.09
A novel switch region regulates H-ras membrane orientation and signal output. EMBO J (2008) 2.06
Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. J Am Chem Soc (2007) 2.04
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc (2004) 2.00
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys (2007) 1.93
Molecular dynamics simulations and drug discovery. BMC Biol (2011) 1.91
Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution. Protein Sci (2004) 1.89
Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB. Proc Natl Acad Sci U S A (2006) 1.86
Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer. J Med Chem (2007) 1.84
Agonist-mediated conformational changes in acetylcholine-binding protein revealed by simulation and intrinsic tryptophan fluorescence. J Biol Chem (2004) 1.81
An unexpected twist in viral capsid maturation. Nature (2009) 1.80
The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers (2003) 1.80
Defining long-range order and local disorder in native alpha-synuclein using residual dipolar couplings. J Am Chem Soc (2005) 1.75
Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci (2006) 1.75
POVME: an algorithm for measuring binding-pocket volumes. J Mol Graph Model (2010) 1.75
Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins. Structure (2008) 1.75
Application of the level-set method to the implicit solvation of nonpolar molecules. J Chem Phys (2007) 1.73
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei. Proc Natl Acad Sci U S A (2008) 1.73
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des (2008) 1.69
Antibacterial drug leads targeting isoprenoid biosynthesis. Proc Natl Acad Sci U S A (2012) 1.69
Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. PLoS Comput Biol (2009) 1.67
A gating mechanism proposed from a simulation of a human alpha7 nicotinic acetylcholine receptor. Proc Natl Acad Sci U S A (2005) 1.66
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc (2007) 1.65
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. J Chem Theory Comput (2012) 1.65
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors. PLoS Comput Biol (2006) 1.65
Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis. J Mol Biol (2005) 1.64
Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Model (2008) 1.64
Water in cavity-ligand recognition. J Am Chem Soc (2010) 1.63
Role of the catalytic triad and oxyanion hole in acetylcholinesterase catalysis: an ab initio QM/MM study. J Am Chem Soc (2002) 1.63
Exploring global motions and correlations in the ribosome. Biophys J (2005) 1.62
The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family. J Mol Biol (2005) 1.60
Thermodynamics reveal that helix four in the NLS of NF-kappaB p65 anchors IkappaBalpha, forming a very stable complex. J Mol Biol (2006) 1.59
Toward a unified representation of protein structural dynamics in solution. J Am Chem Soc (2009) 1.55
Stabilizing IkappaBalpha by "consensus" design. J Mol Biol (2006) 1.53
Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. J Chem Theory Comput (2008) 1.52
How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study. J Am Chem Soc (2005) 1.51
Control of cation permeation through the nicotinic receptor channel. PLoS Comput Biol (2008) 1.51
Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. J Am Chem Soc (2007) 1.49
Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B (2008) 1.45
A thermodynamic switch modulates abscisic acid receptor sensitivity. EMBO J (2011) 1.44
How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput (2010) 1.44
Implementation of Accelerated Molecular Dynamics in NAMD. Comput Sci Discov (2011) 1.44
Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex. J Mol Biol (2008) 1.44
Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution. J Chem Phys (2007) 1.43
The physical basis of microtubule structure and stability. Protein Sci (2003) 1.43
NMR characterization of long-range order in intrinsically disordered proteins. J Am Chem Soc (2010) 1.43
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J (2006) 1.42
Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A (2013) 1.41
Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations. J Am Chem Soc (2009) 1.40
On the role of frustration in the energy landscapes of allosteric proteins. Proc Natl Acad Sci U S A (2011) 1.39
Kinetic enhancement of NF-kappaBxDNA dissociation by IkappaBalpha. Proc Natl Acad Sci U S A (2009) 1.39
Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol (2010) 1.38
Protein conformational flexibility from structure-free analysis of NMR dipolar couplings: quantitative and absolute determination of backbone motion in ubiquitin. Angew Chem Int Ed Engl (2009) 1.38
Increased membrane affinity of the C1 domain of protein kinase Cdelta compensates for the lack of involvement of its C2 domain in membrane recruitment. J Biol Chem (2005) 1.37
The influence of macromolecular crowding on HIV-1 protease internal dynamics. J Am Chem Soc (2006) 1.37
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications. Nucleic Acids Res (2006) 1.37
Amide H/2H exchange reveals communication between the cAMP and catalytic subunit-binding sites in the R(I)alpha subunit of protein kinase A. J Mol Biol (2002) 1.36
Pre-folding IkappaBalpha alters control of NF-kappaB signaling. J Mol Biol (2008) 1.35
Tetrameric mouse acetylcholinesterase: continuum diffusion rate calculations by solving the steady-state Smoluchowski equation using finite element methods. Biophys J (2004) 1.35
Epitope mapping of a monoclonal antibody against human thrombin by H/D-exchange mass spectrometry reveals selection of a diverse sequence in a highly conserved protein. Protein Sci (2002) 1.35
Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys (2011) 1.35
Quantitative determination of the conformational properties of partially folded and intrinsically disordered proteins using NMR dipolar couplings. Structure (2009) 1.33
Allosteric networks in thrombin distinguish procoagulant vs. anticoagulant activities. Proc Natl Acad Sci U S A (2012) 1.33
Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. J Chem Phys (2005) 1.31
Folding landscapes of ankyrin repeat proteins: experiments meet theory. Curr Opin Struct Biol (2008) 1.31
Limitations of atom-centered dielectric functions in implicit solvent models. J Phys Chem B (2005) 1.31
Potent, selective pyrone-based inhibitors of stromelysin-1. J Am Chem Soc (2005) 1.28
Molecular dynamics of acetylcholinesterase. Acc Chem Res (2002) 1.28
Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor. Biophys J (2007) 1.28
Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective. J Mol Biol (2009) 1.27
Ribosome motions modulate electrostatic properties. Biopolymers (2004) 1.27
Intrinsic disorder in measles virus nucleocapsids. Proc Natl Acad Sci U S A (2011) 1.27
Modelling cardiac calcium sparks in a three-dimensional reconstruction of a calcium release unit. J Physiol (2012) 1.26
Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha. Biochemistry (2010) 1.25
Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A (2009) 1.25
The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures. PLoS Comput Biol (2008) 1.25